lammps

History

Axel Kohlmeyer 27d2fab951 simplify processing for "*" in filenames for embedding timestep by using utility function		2022-03-29 06:06:48 -04:00
..
Install.sh	…
README	…
dump_netcdf.cpp	simplify processing for "*" in filenames for embedding timestep by using utility function	2022-03-29 06:06:48 -04:00
dump_netcdf.h	Apply override to remaining classes	2022-01-22 09:56:01 -05:00
dump_netcdf_mpiio.cpp	simplify processing for "*" in filenames for embedding timestep by using utility function	2022-03-29 06:06:48 -04:00
dump_netcdf_mpiio.h	Apply override to remaining classes	2022-01-22 09:56:01 -05:00
netcdf_units.cpp	cosmetic changes (simplify, use constexpr, remove dead code, join wrapped lines)	2021-12-23 01:23:13 -05:00
netcdf_units.h	define and use LMP_MAX_VAR_DIMS instead of NC_MAX_VAR_DIMS to avoid stack overflows	2021-12-26 17:15:13 -05:00

README

NETCDF
============

This package provides the netcdf and netcdf/mpiio dump styles.
See the doc page for dump netcdf or dump netcdf/mpiio command for how to use
them. Compiling these dump styles requires having the netCDF library installed
on your system. See lib/netcdf/README for additional details.

PACKAGE DESCRIPTION
-------------------

This is a LAMMPS (https://www.lammps.org/) dump style for output into a NetCDF
database. The database format follows the AMBER NetCDF trajectory convention
(http://ambermd.org/netcdf/nctraj.xhtml), but includes extensions to this
convention. These extension are:
* A variable "cell_origin" (of dimension "frame", "cell_spatial") that contains
  the bottom left corner of the simulation cell.
* Any number of additional variables corresponding to per atom scalar, vector
  or tensor quantities available within LAMMPS. Tensor quantities are written in
  Voigt notation. An additional dimension "Voigt" of length 6 is created for
  this purpose.
* Possibility to output to an HDF5 database.

NetCDF files can be directly visualized with the following tools:
* Ovito (http://www.ovito.org/). Ovito supports the AMBER convention and all of
  the above extensions.
* VMD (http://www.ks.uiuc.edu/Research/vmd/).
* AtomEye (http://www.libatoms.org/). The libAtoms version of AtomEye contains
  a NetCDF reader that is not present in the standard distribution of AtomEye.

The person who created these files is Lars Pastewka at
the University of Freiburg (lars.pastewka@imtek.uni-freiburg.de).
Contact him directly if you have questions.

Lars Pastewka
University of Freiburg
Department of Microsystems Engineering
Georges-Köhler-Allee 103, 79110 Freiburg, Germany
e-mail: lars.pastewka@imtek.uni-freiburg.de